Technical advances: Genome-wide cDNA-AFLP® analysis of the Arabidopsis transcriptome

OMICS A Journal of Integrative Biology

Volumn 7, Issue 2, 2003, Pages 143-159

  Volkmuth, Wayne ^a   Turk, Stefan ^b   Shapiro, Amy ^a   Fang, Yiwen ^a   Kiegle, Ed ^a   Van Haaren, Mark ^b   Donson, Jonathan ^a  

^a Ceres Inc   (United States)

^b KEYGENE N V   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; PLANT DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARABIDOPSIS; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; DNA MICROARRAY; DNA SEQUENCE; ELECTROPHORETIC MOBILITY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LOCUS; GENETIC TRANSCRIPTION; GENETICS; GENOME; GENOME ANALYSIS; ISOLATION AND PURIFICATION; METHODOLOGY; NONHUMAN; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PLANT GROWTH; PRIORITY JOURNAL; RANDOM AMPLIFIED POLYMORPHIC DNA; REPRODUCIBILITY; RNA ANALYSIS; SEQUENCE HOMOLOGY;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 0037960772     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/153623103322246548     Document Type: Article

References (59)

1. ALTSCHUL, S.F., GISH, W., MILLER, W., et al. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
2. ARABIDOPSIS GENOME INITIATIVE. (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
3. BACHEM, C.W.B., VAN DER HOEVEN, R.S., DE BRUIJN, S.M., et al. (1996). Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J 9, 745-753.
4. BACHEM, C.W.B., OOMEN, R.J.F.J. and VISSER, R.G.F. (1998). Transcript imaging with cDNA-AFLP: a step-by-step protocol. Plant Mol Biol Rep 16, 157-173.
5. BORSANI, O., VALPUESTA, V., and BOTELLA, M.A. (2001). Evidence for a role of salicylic acid in the oxidative damage generated by NaCl and osmotic stress in Arabidopsis seedlings. Plant Physiol 126, 1024-1030.
6. CAO, H., GLAZEBROOK, J., CLARKE, J.D., et al. (1997). The Arabidopsis NPR1 gene that controls systemic acquired resistance encodes a novel protein containing ankyrin repeats. Cell 88, 57-63.
7. CHEN, W., and SINGH, K.B. (1999). The auxin, hydrogen peroxide and salicylic acid induced expression of the Arabidopsis GST6 promoter is mediated in part by an ocs element. Plant J 19, 667-677.
8. CHO, Y., and WALBOT, V. (2001). Computational methods for gene annotation: the Arabidopsis genome. Curr Opin Biotechnol 12, 126-130.
9. COOPER, B. (2001). Collateral gene expression changes induced by distinct plant viruses during the hypersensitive resistance reaction in Chenopodium amaranticolor. Plant J 26, 339-349.
10. DITT, R.F., NESTER, E.W., and COMAI, L. (2001). Plant gene expression response to Agrobacterium tumefaciens. Proc Natl Acad Sci USA 98, 10954-10959.
11. DONG, X., MINDRINOS, M., DAVIS, K.R., et al. (1991). Induction of Arabidopsis defense genes by virulent and avirulent Pseudomonas syringae strains and by a cloned avirulence gene. Plant Cell 3, 61-72.
12. DONG, X., LI, X., ZHANG, Y., et al. (2001). Regulation of systemic acquired resistance by NPR1 and its partners. Novartis Found Symp 236, 165-173; discussion 173-175.
13. DONSON, J., FANG, Y., ESPIRITU-SANTO, G., et al. (2002). Comprehensive gene expression analysis by transcript profiling. Plant Mol Biol 48, 75-97.
14. DU, L., and CHEN, Z. (2000). Identification of genes encoding receptor-like protein kinases as possible targets of pathogen- and salicylic acid-induced WRKY DNA-binding proteins in Arabidopsis. Plant J 24, 837-847.
15. DURRANT, W.E., ROWLAND, O., PIEDRAS, P., et al. (2000). cDNA-AFLP reveals a striking overlap in race-specific resistance and wound response gene expression profiles. Plant Cell 12, 963-977.
16. EISEN, M.B., and BROWN, P.O. (1999). DNA arrays for analysis of gene expression. Methods Enzymol 303, 179-205.
17. FUKUDA, T., KIDO, A., KAJINO, K., et al. (1999). Cloning of differentially expressed genes in highly and low metastatic rat osteosarcomas by a modified cDNA-AFLP method. Biochem Biophys Res Commun 261, 35-40.
18. GAFFNEY, T., FRIEDRICH, L., VERNOOIJ, B., et al. (1993). Requirement of salicylic acid for the induction of systemic acquired resistance. Science 261, 754-756.
19. GIRKE, T., TODD, J., RUUSKA, S., et al. (2000). Microarray analysis of developing Arabidopsis seeds. Plant Physiol 124, 1570-1581.
20. GISH, W., and STATES, D.J. (1993). Identification of protein coding regions by database similarity search. Nat Genet 3, 266-272.
21. GOLDBERG, R.B. (2001). From cot curves to genomics. How gene cloning established new concepts in plant biology. Plant Physiol 125, 4-8.
22. GORLACH, J., VOLRATH, S., KNAUF-BEITER, G., et al. (1996). Benzothiadiazole, a novel class of inducers of systemic acquired resistance, activates gene expression and disease resistance in wheat. Plant Cell 8, 629-643.
23. GRANT, J.J., YUN, B.W., and LOAKE, G.J. (2000). Oxidative burst and cognate redox signalling reported by luciferase imaging: identification of a signal network that functions independently of ethylene, SA and Me-JA but is dependent on MAPKK activity. Plant J 24, 569-582.
24. GUIGÓ, R., AGARWAL, P., ABRIL, J.F., et al. (2000). An assessment of gene prediction accuracy in large DNA sequences. Genome Res 10, 1631-1642.
25. HAAG, E., and RAMAN, V. (1994). Effects of primer choice and source of Taq DNA polymerase on the banding patterns of differential display RT-PCR. Biotechniques 2, 226-228.
26. HUGHES, T.R., MAO, M., JONES, A.R., et al. (2001). Expression profiling using microarrays fabricated by an inkjet oligonucleotide synthesizer. Nat Biotechnol 19, 342-347.
27. HUGHES, T.R., MARTON, M.J., JONES, A.R., et al. (2000). Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
28. KANE, M.D., JATKOE, T.A., STUMPF, C.R., et al. (2000). Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28, 4552-4557.
29. KUC, J. (1982). Induced immunity to plant disease. Bioscience 32, 854-860.
30. LEE, H.S., and CHEN, Z.J. (2001). Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc Natl Acad Sci USA 98, 6753-6758.
31. LIANG, P., and PARDEE, A.B. (1992). Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science, 257, 967-971.
32. LIPSHUTZ, R.J., FODOR, S.P., GINGERAS, T.R., et al. (1999). High-density synthetic oligonucleotide arrays. Nat Genet Suppl 21, 20-24.
33. MATZ, M.V., and LUKYANOV, S.A. (1998). Different strategies of differential display: areas of application. Nucleic Acids Res 26, 5537-5543.
34. McGONIGLE, B., KEELER, S.J., LAU, S-M.C., et al. (2000). A genomics approach to the comprehensive analysis of the glutathione S-transferase gene family in soybean and maize. Plant Physiol 124, 1105-1120.
35. MELAN, M.A., DONG, X., ENDARA, M.E., et al. (1993). An Arabidopsis thaliana lipoxygenase gene can be induced by pathogens, abscisic acid, and methyl jasmonate. Plant Physiol 101, 441-450.
36. MURASHIGE, T., and SKOOG, F. (1962). A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15, 473-497.
37. PAVY, N., ROMBAUTS, S., DEHAIS, P., et al. (1999). Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences. Bioinformatics 11, 887-899.
38. PENN, S.G., RANK, D.R., HANZEL, D.K., et al. (2000). Mining the human genome using microarrays of open reading frames. Nat Genet 26, 315-318.
39. PETERS, J.L., CONSTANDT, H., NEYT, P., et al. (2001). A physical amplified fragment-length polymorphism map of Arabidopsis. Plant Physiol 127, 1579-1589.
40. QIN, L., OVERMARS, H., HELDER, J., et al. (2000). An efficient cDNA-AFLP based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis. Mol Plant Microbe Interact 13, 830-836.
41. QIN, L., PRINS, P., JONES, J.T., et al. (2001). GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP. Nucleic Acids Res 29, 1616-1622.
42. 2. Plant Physiol 115, 137-149.
43. RUBINSTEIN, A.L., LEE, D., LUO, R., et al. (2000). Genes dependent on zebrafish cyclops function identified by AFLP differential gene expression screen. Genesis 26, 86-97.
44. RYALS, J.A., NEUENSCHWANDER, U.H., WILLITS, M.G., et al. (1996). Systemic acquired resistance. Plant Cell 8, 1809-1819.
45. SABLOWSKI, R.W.M., and MEYEROWITZ, E.M. (1998). A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell 92, 93-103.
46. SALUNGA, R.C., GUO, H., LUO, L., et al. (1999). Gene expression analysis via cDNA microarrays of laser capture microdissected cells from fixed tissue. In M. Schena, ed. DNA Microarrays, A Practical Approach (Oxford University Press, New York), pp. 121-137.
47. SAMBROOK, J., and RUSSELL, D.W. (2001). Molecular Cloning: A Laboratory Manual, 3rd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY).
48. SANGER, F., and COULSON, A.R. (1978). The use of thin acrylamide gels for DNA sequencing. FEBS Lett 87, 107-110.
49. SHOEMAKER, D.D., SCHADT, E.E., ARMOUR, C.D., et al. (2001). Experimental annotation of the human genome using microarray technology. Nature 409, 922-927.
50. SPELLMAN, P.T., SHERLOCK, G., ZHANG, M.Q., et al. (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-3297.
51. UKNES, S., MAUCH-MANI, B., MOYER, M., et al. (1992). Acquired resistance in Arabidopsis. Plant Cell 4, 645-656.
52. VOS, P., HOGERS, R., BLEEKER, M., et al. (1995). AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23, 4407-4414.
53. WELSH, J., CHADA, K., DALAL, S.S., et al. (1992). Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Res 20, 4965-4970.
54. YANAI, Y., KAWASAKI, T., SHIMADA, H., et al. (1995). Genomic organization of 251 kDa acetyl-CoA carboxylase genes in Arabidopsis: tandem gene duplication has made two differentially expressed isozymes. Plant Cell Physiol 36, 779-787.
55. YU, D., CHEN, C., and CHEN, Z. (2001). Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression. Plant Cell 13, 1527-1540.
56. ZABEAU, M., and VOS, P. (1993). Selective restriction fragment amplification: a general method for DNA fingerprinting. Eur Patent, 0-534-858-B1.
57. ZABEAU, M., and VOS, P. (2000). Selective restriction fragment amplification: fingerprinting. U.S. Patent, 6,045,994.
58. ZHANG, J.S., DUNCAN, E.L., CHANG, A.C.M., et al. (1998). Differential display of mRNA. Mol Biotechnol 10, 155-165.
59. ZHOU, J.M., TRIFA, Y., SILVA, H., et al. (2000). NPR1 differentially interacts with members of the TGA/OBF family of transcription factors that bind an element of the PR-1 gene required for induction by salicylic acid. Mol Plant Microbe Interact 13, 191-202.